The core class of a multivariate analysis. More...

#include <Bpp/Numeric/Stat/Mva/DualityDiagram.h>

Inheritance diagram for bpp::DualityDiagram:

Collaboration diagram for bpp::DualityDiagram:

Public Member Functions
	DualityDiagram ()
	Build an empty DualityDiagram object.
	DualityDiagram (const Matrix< double > &matrix, const std::vector< double > &rowWeights, const std::vector< double > &colWeights, unsigned int nbAxes, double tol=0.0000001, bool verbose=true) throw (Exception)
	Build a new DualityDiagram object.
virtual	~DualityDiagram ()
DualityDiagram *	clone () const
	Create a copy of this object and send a pointer to it.
void	setData (const Matrix< double > &matrix, const std::vector< double > &rowWeights, const std::vector< double > &colWeights, unsigned int nbAxes, double tol=0.0000001, bool verbose=true) throw (Exception)
	Set the data and perform computations.
std::vector< double >	computeVariancePercentagePerAxis () throw (Exception)
size_t	getNbOfKeptAxes () const throw (Exception)
const std::vector< double >	getRowWeights () const throw (Exception)
const std::vector< double >	getColumnWeights () const throw (Exception)
const std::vector< double > &	getEigenValues () const throw (Exception)
const RowMatrix< double > &	getRowCoordinates () const throw (Exception)
const RowMatrix< double > &	getColCoordinates () const throw (Exception)
const RowMatrix< double > &	getPrincipalAxes () const throw (Exception)
const RowMatrix< double > &	getPrincipalComponents () const throw (Exception)
Private Member Functions
void	check_ (const Matrix< double > &matrix, const std::vector< double > &rowWeights, const std::vector< double > &colWeights, unsigned int nbAxes) throw (Exception)
void	compute_ (const Matrix< double > &matrix, double tol, bool verbose)
Private Attributes
std::vector< double >	rowWeights_
std::vector< double >	colWeights_
size_t	nbAxes_
std::vector< double >	eigenValues_
RowMatrix< double >	eigenVectors_
RowMatrix< double >	rowCoord_
RowMatrix< double >	colCoord_
RowMatrix< double >	ppalAxes_
RowMatrix< double >	ppalComponents_

Detailed Description

The core class of a multivariate analysis.

In the constructor, the eigen values and vectors of the variance-covariance or correlation matrix are calculated. Eigen values and vectors are stored in the eigenValues_ and eigenVectors_ respectively. Furthermore, four matrices are calculated: the row and column coordinates as well as the principal axes and components.

The code of this class is deeply inspired from the R code of the as.dudi function available in the ade4 package.

Definition at line 57 of file DualityDiagram.h.

Constructor & Destructor Documentation

bpp::DualityDiagram::DualityDiagram ( ) [inline]

Build an empty DualityDiagram object.

Definition at line 77 of file DualityDiagram.h.

Referenced by clone().

DualityDiagram::DualityDiagram	(	const Matrix< double > &	matrix,
		const std::vector< double > &	rowWeights,
		const std::vector< double > &	colWeights,
		unsigned int	nbAxes,
		double	tol = `0.0000001`,
		bool	verbose = `true`
	)		throw (Exception)

Build a new DualityDiagram object.

Parameters:

matrix	The input data to analyse.
rowWeights	A vector of values specifying the weights of rows.
colWeights	A vector of values specifying the weights of columns.
nbAxes	The number of kept axes during the analysis.
tol	Tolerance threshold for null eigenvalues (a value less than tol times the first one is considered as null)
verbose	Should warnings be dispayed.

Exceptions:

Exception if an error occured.

Definition at line 50 of file DualityDiagram.cpp.

DualityDiagram::~DualityDiagram ( ) [virtual]

Definition at line 288 of file DualityDiagram.cpp.

Member Function Documentation

void DualityDiagram::check_	(	const Matrix< double > &	matrix,
		const std::vector< double > &	rowWeights,
		const std::vector< double > &	colWeights,
		unsigned int	nbAxes
	)		throw (Exception) `[private]`

Definition at line 70 of file DualityDiagram.cpp.

DualityDiagram* bpp::DualityDiagram::clone ( ) const [inline, virtual]

Create a copy of this object and send a pointer to it.

Returns:: A pointer toward the copy object.

Implements bpp::Clonable.

Reimplemented in bpp::PrincipalComponentAnalysis, and bpp::CorrespondenceAnalysis.

Definition at line 114 of file DualityDiagram.h.

References DualityDiagram().

void DualityDiagram::compute_	(	const Matrix< double > &	matrix,
		double	tol,
		bool	verbose
	)		`[private]`

Definition at line 114 of file DualityDiagram.cpp.

References bpp::ApplicationTools::displayWarning(), bpp::Matrix< Scalar >::getNumberOfColumns(), bpp::Matrix< Scalar >::getNumberOfRows(), bpp::EigenValue< Real >::getRealEigenValues(), bpp::EigenValue< Real >::getV(), bpp::MatrixTools::hadamardMult(), bpp::EigenValue< Real >::isSymmetric(), bpp::MatrixTools::mult(), bpp::RowMatrix< Scalar >::resize(), and bpp::MatrixTools::transpose().

std::vector<double> bpp::DualityDiagram::computeVariancePercentagePerAxis ( ) throw (Exception)

const RowMatrix<double>& bpp::DualityDiagram::getColCoordinates ( ) const throw (Exception) [inline]

Definition at line 151 of file DualityDiagram.h.

References colCoord_.

const std::vector<double> bpp::DualityDiagram::getColumnWeights ( ) const throw (Exception) [inline]

Definition at line 148 of file DualityDiagram.h.

References colWeights_.

const std::vector<double>& bpp::DualityDiagram::getEigenValues ( ) const throw (Exception) [inline]

Definition at line 149 of file DualityDiagram.h.

References eigenValues_.

size_t bpp::DualityDiagram::getNbOfKeptAxes ( ) const throw (Exception) [inline]

Definition at line 146 of file DualityDiagram.h.

References nbAxes_.

const RowMatrix<double>& bpp::DualityDiagram::getPrincipalAxes ( ) const throw (Exception) [inline]

Definition at line 152 of file DualityDiagram.h.

References ppalAxes_.

const RowMatrix<double>& bpp::DualityDiagram::getPrincipalComponents ( ) const throw (Exception) [inline]

Definition at line 153 of file DualityDiagram.h.

References ppalComponents_.

const RowMatrix<double>& bpp::DualityDiagram::getRowCoordinates ( ) const throw (Exception) [inline]

Definition at line 150 of file DualityDiagram.h.

References rowCoord_.

const std::vector<double> bpp::DualityDiagram::getRowWeights ( ) const throw (Exception) [inline]

Definition at line 147 of file DualityDiagram.h.

References rowWeights_.

void DualityDiagram::setData	(	const Matrix< double > &	matrix,
		const std::vector< double > &	rowWeights,
		const std::vector< double > &	colWeights,
		unsigned int	nbAxes,
		double	tol = `0.0000001`,
		bool	verbose = `true`
	)		throw (Exception)

Set the data and perform computations.

Parameters:

matrix	The input data to analyse.
rowWeights	A vector of values specifying the weights of rows.
colWeights	A vector of values specifying the weights of columns.
nbAxes	The number of kept axes during the analysis.
tol	Tolerance threshold for null eigenvalues (a value less than tol times the first one is considered as null)
verbose	Should warnings be dispayed.